SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q90404 from www.uniprot.org...

The NucPred score for your sequence is 0.41 (see score help below)

   1  VPLSPVCGSDGVTYDSECALKLMRCMIQKDLHVVMLSPCKDASPSSVPEL    50
  51  HCSRSVYGCCRDNVTAAQGVGLAGCPSTCECNRYGSYSKTCSPSSGQCSC   100
 101  KPGVGGLKCDRCEPGFWNFRGIVTDEKSGCTPCNCYPLGAVRDDCEQMSG   150
 151  LCSCKAGISGMKCNQCPNGSKLGPSGCDQDPSVSRTCSDLHCQYGATCVQ   200
 201  SIGRAYCECPPSICPKNKQFKVCGSDGVTYANECQLKTIACRQGSVINIL   250
 251  HQGPCQGTTPSTGNIQTTDLTPSPKEHTNLSKIVSLETIPILKAIFPVTD   300
 301  NTTGPQVHKMYTVTASPGVIGHPTAGWPPSSLTSSEPPDLSGSGDFSGDT   350
 351  DLEASGNLEGSGVEPMGFNESSTGPPTPVPNERSTCDNTEFGCCSDGKTP   400
 401  SVDGEGSNCPPTKLFQGVLIVEEVEGQELFYTPEMDDPKSELFGETARSI   450
 451  ENALNELFGNSNVKKDFKSVRVHGLGPSDPVRIIVEVHFDPRTSYNSHDV   500
 501  QRALLQQVKQSRRKSIVVKKPEQDNVKIVDFDWAPLLFTTTSTTAARTTV   550
 551  PITTASALPVTRRPPPATTRWPKVLPHAKVPSTTTKPATTRRPPFSRKVE   600
 601  VRPATVKVHRPCDSQPCLHGGTCEDDGVSYTCSCPAGRGGAVCERTIVYF   650
 651  IPEFGGRSYLAFKTMKAYYTVRISMEFRASNLDGLPLVQWTEKGKGLHFY   700
 701  RPSEGYVELRFNHGVWDGVITSKTLIKPGNWHHVVGNRNRRSGMLSVDGE   750
 751  PHLIGESPPGTDGLNLDTDLFLGGTPEDEMTLVTERTTATKGLQGCIRLL   800
 801  DVNNLIYDLQERSNDVLYGSGVGECGNNPCSPNPCKNRGKCHMKEAEMFH   850
 851  CESVGEFSGPTCADKHNPCDPNPCHQSANCMVLPEGGSKCECPMGREGEL   900
 901  CERVSEAEQDQGKAFIPEFNGLSYLEMNGIHTFVSDLLQKLSMEVIFLAK   950
 951  DPNGMIFYNGQKTDGRGDFVSLNLRDGYLEFKYDLGKGAAVLRSKAPIPL  1000
1001  NVWNVVTVERNGRKGLMKINKDELVSGESPKSRKAPHTALNLKEAFYVGG  1050
1051  APDFNKFARAAGIISGFTGAIQKLSLKSIPLLKKENIRNAMEISNFRWHA  1100
1101  CTKTRNPCQNGGVCSPRLREYDCMCQRGFSGPQCEKALEEKSASGSESVA  1150
1151  FNGRTFIEYHNTVTRSEKAVQVNYFEMSIKTEATKGLILWSGKIAEKSDY  1200
1201  IALAVVDGFVQMTYDLGSKPVTLRSTIPVNTNQWVRIKANRIHGYGTLQV  1250
1251  GNEAPVTGSSPFAATQLDTDGALWLGGIEKLAPGNRLPKAYSTGFIGCIK  1300
1301  DVVIDRQELQLVEDALNNPTILHCPAKK                        1328

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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